chr16-67662541-G-A
Variant summary
Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BP4_StrongBS2
The NM_001037281.2(PARD6A):c.932G>A(p.Arg311Gln) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000428 in 1,613,018 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 15/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_001037281.2 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -8 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
PARD6A | NM_001037281.2 | c.932G>A | p.Arg311Gln | missense_variant | 3/3 | ENST00000458121.7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PARD6A | ENST00000458121.7 | c.932G>A | p.Arg311Gln | missense_variant | 3/3 | 1 | NM_001037281.2 | A1 | |
PARD6A | ENST00000219255.3 | c.935G>A | p.Arg312Gln | missense_variant | 3/3 | 1 | P4 | ||
PARD6A | ENST00000602551.5 | c.845G>A | p.Arg282Gln | missense_variant | 3/3 | 5 | |||
PARD6A | ENST00000602727.1 | n.1092G>A | non_coding_transcript_exon_variant | 2/2 | 2 |
Frequencies
GnomAD3 genomes AF: 0.0000394 AC: 6AN: 152192Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000521 AC: 13AN: 249756Hom.: 0 AF XY: 0.0000517 AC XY: 7AN XY: 135398
GnomAD4 exome AF: 0.0000431 AC: 63AN: 1460826Hom.: 0 Cov.: 32 AF XY: 0.0000385 AC XY: 28AN XY: 726718
GnomAD4 genome AF: 0.0000394 AC: 6AN: 152192Hom.: 0 Cov.: 33 AF XY: 0.0000404 AC XY: 3AN XY: 74346
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Apr 27, 2023 | The c.935G>A (p.R312Q) alteration is located in exon 3 (coding exon 3) of the PARD6A gene. This alteration results from a G to A substitution at nucleotide position 935, causing the arginine (R) at amino acid position 312 to be replaced by a glutamine (Q). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at